MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Value Type	Gene	description	Rank	Interaction Map	Network Comparison Type	Filtered	red	green	network_comparison

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Showing element 1680 to 1729 of 3228 in total

Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1

description	Rank	red	green	network_comparison
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	2246	223.58	224.943	1.0061
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	305	242.339	266.986	1.1017
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]	487	226.313	243.03	1.07387
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]	1985	219.26	217.193	1.00952
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	2477	216.177	216.801	1.00289
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	296	241.282	266.12	1.10294
mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]	3016	0.00001	0.00001	1
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	663	229.072	216.576	1.0577
mitochondrial solute carrier protein. [refseq;acc:nm_016612]	2915	0.00001	0.00001	1
mitochondrial solute carrier protein. [refseq;acc:nm_145305]	27	58	44	1.31818
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	932	225.939	218.013	1.03636
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482]	2168	215.929	214.486	1.00673
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	1263	171.231	167.177	1.02425
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]	1274
mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361]	2159	215.921	214.474	1.00675
mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]	3084	0.00001	0.00001	1
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	2174	215.925	214.481	1.00673
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382]	2163
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318]	1489	213.251	209.264	1.01905
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	2273	213.015	211.858	1.00546
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]	2342	229.258	230.294	1.00452
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	1273	171.231	167.177	1.02425
mitotic checkpoint protein bub3. [swissprot;acc:o43684]	1632	221.934	218.658	1.01498
mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566]	1707	221.283	218.334	1.01351
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257]	2265	211.597	210.416	1.00561
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	995	219.656	212.547	1.03345
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	462	254.434	236.224	1.07709
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	1524	219.306	223.179	1.01766
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]	1527
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	2270	207.54	208.69	1.00554
mo25 protein (cgi-66). [swissprot;acc:q9y376]	2976	0.00001	0.00001	1
mo25-like protein. [swissprot;acc:q9h9s4]	3116
mob-lak. [refseq;acc:nm_130807]	2812
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]	2662	204.768	204.549	1.00107
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]	2667
mondoa. [refseq;acc:nm_014938]	2800	0.00001	0.00001	1
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	2560	202.395	202.042	1.00175
mosaic protein lgn. [swissprot;acc:p81274]	158	249.663	298.263	1.19466
mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797]	2373	212.724	213.574	1.004
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]	2372
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]	2375
mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]	1440	225.039	229.573	1.02015
mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717]	2382	212.724	213.574	1.004
mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]	2381
mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [swissprot;acc:o95405]	2887	0.00001	0.00001	1
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	264	219.421	196.978	1.11394
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]	1578	222.585	218.982	1.01645
mstp028 protein. [refseq;acc:nm_031954]	1197	219.042	213.6	1.02548
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	1465	217.351	213.18	1.01957
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]	741	223.58	235.027	1.0512

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.